The Canaries were holding a 1-0 lead before a late penalty awarded against Kei Kamara sparked Arsenal's comeback.
Hughton felt Norwich had not been given the rub of the green by the officials.
He said: "My first thought is that it was not a corner in the first place, but what I am more aggrieved about is there is contact with Kei, but he swivels and plays the ball.
"You have a linesman who makes a decision from 40 or 50 yards away and the referee who is eight yards away and has the perfect view.
"Their third goal was also offside.
"I have had a private conversation with the referee, but I am still not convinced."